Many parts of Thomas’s works/ideas/stuff has been vetted by the Church in one way or another. I would not sit down myself and sift through his texts and decide, “Ooh, I don’t like that one,” because for all I know I might be getting myself into some trouble.
My advice is, for those things that you are having trouble with, read about them in the CCC and other Magisterial documents. Try, as much as possible, to reconcile them before trashing Thomas (although I’m not saying you’ve trashed him).
Well…
For starters, Aquinas’ embryology is wrong. Like downright plain wrong. Like as in if you agree with it you are disagreeing with what the Church now says (n.b. Aquinas thought ensoulment of the intellectual soul, which is the unique, immortal one created by God, came at some point post-conception, which would make an embryo non-human until that point (this is perfectly consistent with his Aristotelian base). The Church now says that a person is fully human at the point of conception).
Also, Aquinas thought that only priests should be able to touch the Eucharist, and the Church never adopted this (despite what you hear from
some Catholic circles) and allows Deacons (a basically blanket) permission to distribute the Hosts.
Personally, I have read some Aquinas (second half of the SCG Book II, some parts of the ST that have come up in research, and his Commentary of De Trinitate q. 5-6). I find it all very complex, and I’m not sure how useful some of his stuff is practically. Much of his writing is littered with unnatural or uncommon use of phrases and words (in the English language at least).
The other big one is one that affects all major metaphysical systems: Is the world actually like that? Is the world full of matters and forms or is that just a useful metaphor for describing it? Sure, the soul being the form of the body works a little better than Cartesian dualism, but is that how things
actually are? In the world? Maybe, maybe not.
That’s always been my biggest disappointment with metaphysics as a whole. You can pretty much form any sort of internally coherent system in your head to explain how the world works, and it doesn’t necessarily mean anything. Is the world made of 4 elements? Matter and form? Material stuff and immaterial minds? Noumena? Monads? Is it all in God’s mind? Or are we all in the Matrix? This is the problem of the underdetermination of the senses.
In the end, it really doesn’t seem to matter. That’s what I’ve gotten from Thomas à Kempis at least. We aren’t going to be judged by how much we know or understand (because that’s just Pelagianism).